PercolatorFeatureSetHelper Class Reference

Percolator feature set and integration helper. More...

#include <OpenMS/ANALYSIS/ID/PercolatorFeatureSetHelper.h>

Classes
struct	lq_ProteinHit
	For accession dependent sorting of ProteinHits. More...

Static Public Member Functions
static void	mergeMULTISEProteinIds (std::vector< ProteinIdentification > &all_protein_ids, std::vector< ProteinIdentification > &new_protein_ids)
	mergeMULTISEProteinIds
static void	addMSGFFeatures (PeptideIdentificationList &peptide_ids, StringList &feature_set)
	addMSGFFeatures
static void	addXTANDEMFeatures (PeptideIdentificationList &peptide_ids, StringList &feature_set)
	addXTANDEMFeatures
static void	addCOMETFeatures (PeptideIdentificationList &peptide_ids, StringList &feature_set)
	addCOMETFeatures
static void	addANDESFeatures (PeptideIdentificationList &peptide_ids, StringList &feature_set)
	addANDESFeatures
static void	addMASCOTFeatures (PeptideIdentificationList &peptide_ids, StringList &feature_set)
	addMASCOTFeatures
static void	checkExtraFeatures (const std::vector< PeptideHit > &psms, StringList &extra_features)
	checkExtraFeatures
static void	addMSFRAGGERFeatures (StringList &extra_features)
	addMSFraggerFeatures

Static Protected Member Functions
static double	rescaleFragmentFeature_ (double featureValue, int NumMatchedMainIons)
	Rescales the fragment features to penalize features calculated by few ions, adapted from MSGFtoPercolator.
static void	assignDeltaScore_ (std::vector< PeptideHit > &hits, const std::string &score_ref, const std::string &output_ref)
	helper function for assigning the frequently occurring feature delta score

Detailed Description

Percolator feature set and integration helper.

This class contains functions to handle (compute, aggregate, integrate) Percolator features. This includes the calculation or extraction of Percolator features depending on the search engine(s) for later use with PercolatorAdapter. It also includes handling the reintegration of the percolator result into the set of Identifications.

Member Function Documentation

addANDESFeatures()

static void addANDESFeatures ( PeptideIdentificationList &  peptide_ids, StringList &  feature_set  )

static

addANDESFeatures

Parameters

[in]	peptide_ids	PeptideIdentification vector to create Percolator features in
[in]	feature_set	register of added features

Collects and registers the andes search engine specific Percolator features. andes annotates every PSM with its own numeric features as MetaValues named with the "andes:" prefix (e.g. "andes:RankScore", "andes:RawScore", ...). Rather than hard-coding the (currently 47) feature names here, all numeric "andes:"-prefixed MetaValues found on the hits are collected, keeping the andes side the single source of truth for its feature set.

addCOMETFeatures()

static void addCOMETFeatures ( PeptideIdentificationList &  peptide_ids, StringList &  feature_set  )

static

addCOMETFeatures

Parameters

[in]	peptide_ids	PeptideIdentification vector to create Percolator features in
[in]	feature_set	register of added features

Creates and adds Comet specific Percolator features and registers them in feature_set

addMASCOTFeatures()

static void addMASCOTFeatures ( PeptideIdentificationList &  peptide_ids, StringList &  feature_set  )

static

addMASCOTFeatures

Parameters

[in]	peptide_ids	PeptideIdentification vector to create Percolator features in
[in]	feature_set	register of added features

Creates and adds Mascot specific Percolator features and registers them in feature_set

addMSFRAGGERFeatures()

static void addMSFRAGGERFeatures ( StringList &  extra_features )

static

addMSFraggerFeatures

Parameters

[in]

extra_features

register of added features

Registers the MSFragger specific Percolator features in extra_features.

addMSGFFeatures()

static void addMSGFFeatures ( PeptideIdentificationList &  peptide_ids, StringList &  feature_set  )

static

addMSGFFeatures

Parameters

[in]	peptide_ids	PeptideIdentification vector to create Percolator features in
[in]	feature_set	register of added features

Creates and adds MSGF+ specific Percolator features and registers them in feature_set. MSGF+ should be run with the addFeatures flag enabled.

addXTANDEMFeatures()

static void addXTANDEMFeatures ( PeptideIdentificationList &  peptide_ids, StringList &  feature_set  )

static

addXTANDEMFeatures

Parameters

[in]	peptide_ids	PeptideIdentification vector to create Percolator features in
[in]	feature_set	register of added features

Creates and adds X!Tandem specific Percolator features and registers them in feature_set

assignDeltaScore_()

static void assignDeltaScore_ ( std::vector< PeptideHit > &  hits, const std::string &  score_ref, const std::string &  output_ref  )

staticprotected

helper function for assigning the frequently occurring feature delta score

checkExtraFeatures()

static void checkExtraFeatures ( const std::vector< PeptideHit > &  psms, StringList &  extra_features  )

static

checkExtraFeatures

Parameters

[in]	psms	the vector of PeptideHit to be checked
[in]	extra_features	the list of requested extra features

checks and removes requested extra Percolator features that are actually unavailable (to compute)

mergeMULTISEProteinIds()

static void mergeMULTISEProteinIds ( std::vector< ProteinIdentification > &  all_protein_ids, std::vector< ProteinIdentification > &  new_protein_ids  )

static

mergeMULTISEProteinIds

Parameters

[in]	all_protein_ids	ProteinIdentification vector to be merged into
[in]	new_protein_ids	ProteinIdentification vector to merge

Merges a ProteinIdentification run into another: takes over the search parameters of the first run, sets the search engine to "multiple" once runs from differing search engines are combined, and unions the ProteinHits by accession.

rescaleFragmentFeature_()

static double rescaleFragmentFeature_ ( double  featureValue, int  NumMatchedMainIons  )

staticprotected

Rescales the fragment features to penalize features calculated by few ions, adapted from MSGFtoPercolator.